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libsbml.ModelDefinition Class Reference
Inheritance diagram for libsbml.ModelDefinition:
[legend]

Detailed Description

{comp}

comp Implementation of the ModelDefinition construct from the “comp” package.

The Hierarchical Model Composition package (“comp”) allows multiple Model objects to be defined in a single SBMLDocument. While these new Model objects are not new SBML classes, they are given a new name, <modelDefinition>, and reside in ListOfModelDefinition objects. In libSBML, this class inherits from the Model class, changing only the expected parent of the object, and the XML name.

An additional restriction is placed on the 'id' attribute of ModelDefinition objects: not only must it be unique across all such attributes of type SId within the ModelDefintion, it must also be unique across all Model, ModelDefinition, and ExternalModelDefinition objects in the same SBMLDocument.

Public Member Functions

def addCompartment
 
def addCompartmentType
 
def addConstraint
 
def addCVTerm
 
def addEvent
 
def addFunctionDefinition
 
def addInitialAssignment
 
def addParameter
 
def addReaction
 
def addRule
 
def addSpecies
 
def addSpeciesType
 
def addUnitDefinition
 
def appendAnnotation
 
def appendFrom
 
def appendNotes
 
def clone
 
def createAlgebraicRule
 
def createAssignmentRule
 
def createCompartment
 
def createCompartmentType
 
def createConstraint
 
def createDelay
 
def createEvent
 
def createEventAssignment
 
def createFunctionDefinition
 
def createInitialAssignment
 
def createKineticLaw
 
def createKineticLawLocalParameter
 
def createKineticLawParameter
 
def createModifier
 
def createParameter
 
def createProduct
 
def createRateRule
 
def createReactant
 
def createReaction
 
def createSpecies
 
def createSpeciesType
 
def createTrigger
 
def createUnit
 
def createUnitDefinition
 
def disablePackage
 
def enablePackage
 
def getAncestorOfType
 
def getAnnotation
 
def getAnnotationString
 
def getAreaUnits
 
def getAssignmentRule
 
def getAssignmentRuleByVariable
 
def getColumn
 
def getCompartment
 
def getCompartmentType
 
def getConstraint
 
def getConversionFactor
 
def getCVTerm
 
def getCVTerms
 
def getElementByMetaId
 
def getElementBySId
 
def getElementName
 
def getEvent
 
def getExtentUnits
 
def getFunctionDefinition
 
def getId
 
def getInitialAssignment
 
def getInitialAssignmentBySymbol
 
def getLengthUnits
 
def getLevel
 
def getLine
 
def getListOfAllElements
 
def getListOfAllElementsFromPlugins
 
def getListOfCompartments
 
def getListOfCompartmentTypes
 
def getListOfConstraints
 
def getListOfEvents
 
def getListOfFunctionDefinitions
 
def getListOfInitialAssignments
 
def getListOfParameters
 
def getListOfReactions
 
def getListOfRules
 
def getListOfSpecies
 
def getListOfSpeciesTypes
 
def getListOfUnitDefinitions
 
def getMetaId
 
def getModel
 
def getModelHistory
 
def getModifierSpeciesReference
 
def getName
 
def getNamespaces
 
def getNotes
 
def getNotesString
 
def getNumCompartments
 
def getNumCompartmentTypes
 
def getNumConstraints
 
def getNumCVTerms
 
def getNumEvents
 
def getNumFunctionDefinitions
 
def getNumInitialAssignments
 
def getNumParameters
 
def getNumPlugins
 
def getNumReactions
 
def getNumRules
 
def getNumSpecies
 
def getNumSpeciesTypes
 
def getNumSpeciesWithBoundaryCondition
 
def getNumUnitDefinitions
 
def getPackageName
 
def getPackageVersion
 
def getParameter
 
def getParentSBMLObject
 
def getPlugin
 
def getPrefix
 
def getRateRule
 
def getRateRuleByVariable
 
def getReaction
 
def getResourceBiologicalQualifier
 
def getResourceModelQualifier
 
def getRule
 
def getRuleByVariable
 
def getSBMLDocument
 
def getSBOTerm
 
def getSBOTermAsURL
 
def getSBOTermID
 
def getSpecies
 
def getSpeciesReference
 
def getSpeciesType
 
def getSubstanceUnits
 
def getTimeUnits
 
def getTypeCode
 
def getUnitDefinition
 
def getURI
 
def getVersion
 
def getVolumeUnits
 
def hasRequiredElements
 
def hasValidLevelVersionNamespaceCombination
 
def isPackageEnabled
 
def isPackageURIEnabled
 
def isPkgEnabled
 
def isPkgURIEnabled
 
def isPopulatedListFormulaUnitsData
 
def isSetAnnotation
 
def isSetAreaUnits
 
def isSetConversionFactor
 
def isSetExtentUnits
 
def isSetId
 
def isSetLengthUnits
 
def isSetMetaId
 
def isSetModelHistory
 
def isSetName
 
def isSetNotes
 
def isSetSBOTerm
 
def isSetSubstanceUnits
 
def isSetTimeUnits
 
def isSetVolumeUnits
 
def matchesRequiredSBMLNamespacesForAddition
 
def matchesSBMLNamespaces
 
def populateListFormulaUnitsData
 
def removeCompartment
 
def removeCompartmentType
 
def removeConstraint
 
def removeEvent
 
def removeFromParentAndDelete
 
def removeFunctionDefinition
 
def removeInitialAssignment
 
def removeParameter
 
def removeReaction
 
def removeRule
 
def removeSpecies
 
def removeSpeciesType
 
def removeTopLevelAnnotationElement
 
def removeUnitDefinition
 
def renameIDs
 
def renameMetaIdRefs
 
def renameSIdRefs
 
def renameUnitSIdRefs
 
def replaceTopLevelAnnotationElement
 
def setAnnotation
 
def setAreaUnits
 
def setConversionFactor
 
def setExtentUnits
 
def setId
 
def setLengthUnits
 
def setMetaId
 
def setModelHistory
 
def setName
 
def setNamespaces
 
def setNotes
 
def setSBOTerm
 
def setSubstanceUnits
 
def setTimeUnits
 
def setVolumeUnits
 
def toSBML
 
def toXMLNode
 
def unsetAnnotation
 
def unsetAreaUnits
 
def unsetConversionFactor
 
def unsetCVTerms
 
def unsetExtentUnits
 
def unsetId
 
def unsetLengthUnits
 
def unsetMetaId
 
def unsetModelHistory
 
def unsetName
 
def unsetNotes
 
def unsetSBOTerm
 
def unsetSubstanceUnits
 
def unsetTimeUnits
 
def unsetVolumeUnits
 

Member Function Documentation

def libsbml.Model.addCompartment (   self,
  args 
)
inherited

Python method signature(s):

addCompartment(Model self, Compartment c)   int

Adds a copy of the given Compartment object to this Model.

Parameters
cthe Compartment object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createCompartment()
def libsbml.Model.addCompartmentType (   self,
  args 
)
inherited

Python method signature(s):

addCompartmentType(Model self, CompartmentType ct)   int

Adds a copy of the given CompartmentType object to this Model.

Parameters
ctthe CompartmentType object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
See also
createCompartmentType()
def libsbml.Model.addConstraint (   self,
  args 
)
inherited

Python method signature(s):

addConstraint(Model self, Constraint c)   int

Adds a copy of the given Constraint object to this Model.

Parameters
cthe Constraint object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createConstraint()
def libsbml.SBase.addCVTerm (   self,
  args 
)
inherited

Python method signature(s):

addCVTerm(SBase self, CVTerm term, bool newBag=False)   int
addCVTerm(SBase self, CVTerm term)   int

Adds a copy of the given CVTerm object to this SBML object.

Parameters
termthe CVTerm to assign.
newBagif True, creates a new RDF bag with the same identifier as a previous bag, and if False, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
def libsbml.Model.addEvent (   self,
  args 
)
inherited

Python method signature(s):

addEvent(Model self, Event e)   int

Adds a copy of the given Event object to this Model.

Parameters
ethe Event object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createEvent()
def libsbml.Model.addFunctionDefinition (   self,
  args 
)
inherited

Python method signature(s):

addFunctionDefinition(Model self, FunctionDefinition fd)   int

Adds a copy of the given FunctionDefinition object to this Model.

Parameters
fdthe FunctionDefinition to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createFunctionDefinition()
def libsbml.Model.addInitialAssignment (   self,
  args 
)
inherited

Python method signature(s):

addInitialAssignment(Model self, InitialAssignment ia)   int

Adds a copy of the given InitialAssignment object to this Model.

Parameters
iathe InitialAssignment object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createInitialAssignment()
def libsbml.Model.addParameter (   self,
  args 
)
inherited

Python method signature(s):

addParameter(Model self, Parameter p)   int

Adds a copy of the given Parameter object to this Model.

Parameters
pthe Parameter object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createParameter()
def libsbml.Model.addReaction (   self,
  args 
)
inherited

Python method signature(s):

addReaction(Model self, Reaction r)   int

Adds a copy of the given Reaction object to this Model.

Parameters
rthe Reaction object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createReaction()
def libsbml.Model.addRule (   self,
  args 
)
inherited

Python method signature(s):

addRule(Model self, Rule r)   int

Adds a copy of the given Rule object to this Model.

Parameters
rthe Rule object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createAlgebraicRule()
createAssignmentRule()
createRateRule()
def libsbml.Model.addSpecies (   self,
  args 
)
inherited

Python method signature(s):

addSpecies(Model self, Species s)   int

Adds a copy of the given Species object to this Model.

Parameters
sthe Species object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createSpecies()
def libsbml.Model.addSpeciesType (   self,
  args 
)
inherited

Python method signature(s):

addSpeciesType(Model self, SpeciesType st)   int

Adds a copy of the given SpeciesType object to this Model.

Parameters
stthe SpeciesType object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
See also
createSpeciesType()
def libsbml.Model.addUnitDefinition (   self,
  args 
)
inherited

Python method signature(s):

addUnitDefinition(Model self, UnitDefinition ud)   int

Adds a copy of the given UnitDefinition object to this Model.

Parameters
udthe UnitDefinition object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
See also
createUnitDefinition()
def libsbml.Model.appendAnnotation (   self,
  args 
)
inherited

Python method signature(s):

appendAnnotation(Model self, XMLNode annotation)   int
appendAnnotation(Model self, string annotation)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
appendAnnotation(XMLNode annotation)

Appends annotation content to any existing content in the 'annotation' subelement of this object.

The content in annotation is copied. Unlike setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setAnnotation()

Method variant with the following signature:
appendAnnotation(string annotation)

Appends annotation content to any existing content in the 'annotation' subelement of this object.

The content in annotation is copied. Unlike setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML string that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setAnnotation()
def libsbml.Model.appendFrom (   self,
  args 
)
inherited

Python method signature(s):

appendFrom(Model self, Model model)   int

Takes the contents of the passed-in Model, makes copies of everything, and appends those copies to the appropriate places in this Model.

This method also calls the appendFrom method on all libSBML plug-in objects. 

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
modelthe Model to merge with this one.
def libsbml.SBase.appendNotes (   self,
  args 
)
inherited

Python method signature(s):

appendNotes(SBase self, XMLNode notes)   int
appendNotes(SBase self, string notes)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
appendNotes(string notes)

Appends the given notes to the 'notes' subelement of this object.

The content of the parameter notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML string that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:
appendNotes(XMLNode notes)

Appends the given notes to the 'notes' subelement of this object.

The content of notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML node structure that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.ModelDefinition.clone (   self)

{comp}

comp Implementation of the ModelDefinition construct from the “comp” package.

The Hierarchical Model Composition package (“comp”) allows multiple Model objects to be defined in a single SBMLDocument. While these new Model objects are not new SBML classes, they are given a new name, <modelDefinition>, and reside in ListOfModelDefinition objects. In libSBML, this class inherits from the Model class, changing only the expected parent of the object, and the XML name.

An additional restriction is placed on the 'id' attribute of ModelDefinition objects: not only must it be unique across all such attributes of type SId within the ModelDefintion, it must also be unique across all Model, ModelDefinition, and ExternalModelDefinition objects in the same SBMLDocument. Python method signature(s):

clone(ModelDefinition self)   ModelDefinition

Creates and returns a deep copy of this ModelDefinition object.

Returns
a (deep) copy of this ModelDefinition object
def libsbml.Model.createAlgebraicRule (   self)
inherited

Python method signature(s):

createAlgebraicRule(Model self)   AlgebraicRule

Creates a new AlgebraicRule inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the AlgebraicRule object created
See also
addRule()
def libsbml.Model.createAssignmentRule (   self)
inherited

Python method signature(s):

createAssignmentRule(Model self)   AssignmentRule

Creates a new AssignmentRule inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the AssignmentRule object created
See also
addRule()
def libsbml.Model.createCompartment (   self)
inherited

Python method signature(s):

createCompartment(Model self)   Compartment

Creates a new Compartment inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the Compartment object created
See also
addCompartment()
def libsbml.Model.createCompartmentType (   self)
inherited

Python method signature(s):

createCompartmentType(Model self)   CompartmentType

Creates a new CompartmentType inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the CompartmentType object created
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
See also
addCompartmentType()
def libsbml.Model.createConstraint (   self)
inherited

Python method signature(s):

createConstraint(Model self)   Constraint

Creates a new Constraint inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the Constraint object created
See also
addConstraint()
def libsbml.Model.createDelay (   self)
inherited

Python method signature(s):

createDelay(Model self)   Delay

Creates a new Delay inside the last Event object created in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new Delay is not created and None is returned instead.

Returns
the Delay object created
def libsbml.Model.createEvent (   self)
inherited

Python method signature(s):

createEvent(Model self)   Event

Creates a new Event inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the Event object created
def libsbml.Model.createEventAssignment (   self)
inherited

Python method signature(s):

createEventAssignment(Model self)   EventAssignment

Creates a new EventAssignment inside the last Event object created in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new EventAssignment is not created and None is returned instead.

Returns
the EventAssignment object created
def libsbml.Model.createFunctionDefinition (   self)
inherited

Python method signature(s):

createFunctionDefinition(Model self)   FunctionDefinition

Creates a new FunctionDefinition inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the FunctionDefinition object created
See also
addFunctionDefinition()
def libsbml.Model.createInitialAssignment (   self)
inherited

Python method signature(s):

createInitialAssignment(Model self)   InitialAssignment

Creates a new InitialAssignment inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the InitialAssignment object created
See also
addInitialAssignment()
def libsbml.Model.createKineticLaw (   self)
inherited

Python method signature(s):

createKineticLaw(Model self)   KineticLaw

Creates a new KineticLaw inside the last Reaction object created in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, or a Reaction exists but already has a KineticLaw, a new KineticLaw is not created and None is returned instead.

Returns
the KineticLaw object created
def libsbml.Model.createKineticLawLocalParameter (   self)
inherited

Python method signature(s):

createKineticLawLocalParameter(Model self)   LocalParameter

Creates a new LocalParameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The last KineticLaw object in this Model could have been created in a variety of ways. For example, it could have been added using createKineticLaw(), or it could be the result of using Reaction.createKineticLaw() on the Reaction object created by a createReaction(). If a Reaction does not exist for this model, or the last Reaction does not contain a KineticLaw object, a new Parameter is not created and None is returned instead.

Returns
the Parameter object created
def libsbml.Model.createKineticLawParameter (   self)
inherited

Python method signature(s):

createKineticLawParameter(Model self)   Parameter

Creates a new local Parameter inside the KineticLaw object of the last Reaction created inside this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The last KineticLaw object in this Model could have been created in a variety of ways. For example, it could have been added using createKineticLaw(), or it could be the result of using Reaction.createKineticLaw() on the Reaction object created by a createReaction(). If a Reaction does not exist for this model, or the last Reaction does not contain a KineticLaw object, a new Parameter is not created and None is returned instead.

Returns
the Parameter object created
def libsbml.Model.createModifier (   self)
inherited

Python method signature(s):

createModifier(Model self)   ModifierSpeciesReference

Creates a new ModifierSpeciesReference object for a modifier species inside the last Reaction object in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new ModifierSpeciesReference is not created and None is returned instead.

Returns
the SpeciesReference object created
def libsbml.Model.createParameter (   self)
inherited

Python method signature(s):

createParameter(Model self)   Parameter

Creates a new Parameter inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the Parameter object created
See also
addParameter()
def libsbml.Model.createProduct (   self)
inherited

Python method signature(s):

createProduct(Model self)   SpeciesReference

Creates a new SpeciesReference object for a product inside the last Reaction object in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and None is returned instead.

Returns
the SpeciesReference object created
def libsbml.Model.createRateRule (   self)
inherited

Python method signature(s):

createRateRule(Model self)   RateRule

Creates a new RateRule inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the RateRule object created
See also
addRule()
def libsbml.Model.createReactant (   self)
inherited

Python method signature(s):

createReactant(Model self)   SpeciesReference

Creates a new SpeciesReference object for a reactant inside the last Reaction object in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Reaction object was created and added to this Model is not significant. It could have been created in a variety of ways, for example using createReaction(). If a Reaction does not exist for this model, a new SpeciesReference is not created and None is returned instead.

Returns
the SpeciesReference object created
def libsbml.Model.createReaction (   self)
inherited

Python method signature(s):

createReaction(Model self)   Reaction

Creates a new Reaction inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the Reaction object created
See also
addReaction()
def libsbml.Model.createSpecies (   self)
inherited

Python method signature(s):

createSpecies(Model self)   Species

Creates a new Species inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the Species object created
See also
addSpecies()
def libsbml.Model.createSpeciesType (   self)
inherited

Python method signature(s):

createSpeciesType(Model self)   SpeciesType

Creates a new SpeciesType inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the SpeciesType object created
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
See also
addSpeciesType()
def libsbml.Model.createTrigger (   self)
inherited

Python method signature(s):

createTrigger(Model self)   Trigger

Creates a new Trigger inside the last Event object created in this Model, and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the last Event object in this model was created is not significant. It could have been created in a variety of ways, for example by using createEvent(). If no Event object exists in this Model object, a new Trigger is not created and None is returned instead.

Returns
the Trigger object created
def libsbml.Model.createUnit (   self)
inherited

Python method signature(s):

createUnit(Model self)   Unit

Creates a new Unit object within the last UnitDefinition object created in this model and returns a pointer to it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

The mechanism by which the UnitDefinition was created is not significant. If a UnitDefinition object does not exist in this model, a new Unit is not created and None is returned instead.

Returns
the Unit object created
See also
addUnitDefinition()
def libsbml.Model.createUnitDefinition (   self)
inherited

Python method signature(s):

createUnitDefinition(Model self)   UnitDefinition

Creates a new UnitDefinition inside this Model and returns it.

The SBML Level and Version of the enclosing Model object, as well as any SBML package namespaces, are used to initialize this object's corresponding attributes.

Returns
the UnitDefinition object created
See also
addUnitDefinition()
def libsbml.SBase.disablePackage (   self,
  args 
)
inherited

Python method signature(s):

disablePackage(SBase self, string pkgURI, string pkgPrefix)   int

Disables the given SBML Level 3 package on this object.

This method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from another SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:

import sys
import os.path
from libsbml import *

# We read in an SBML L3V1 model that uses the 'comp' package namespace
doc = readSBML('sbml-file-with-comp-elements.xml');

# We extract one of the species from the model we just read in.
s1 = doc.getModel().getSpecies(0);

# We construct a new model.  This model does not use the 'comp' package.
newDoc = SBMLDocument(3, 1);
newModel = newDoc.createModel();

# The following would fail with an error, because addSpecies() would
# first check that the parent of the given object has namespaces
# declared, and will discover that s1 does but newModel does not.

# newModel.addSpecies(s1);

# However, if we disable the 'comp' package on s1, then the call
# to addSpecies will work.

s1.disablePackage('http://www.sbml.org/sbml/level3/version1/comp/version1',
          'comp');
newModel.addSpecies(s1);
Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
enablePackage()
def libsbml.SBase.enablePackage (   self,
  args 
)
inherited

Python method signature(s):

enablePackage(SBase self, string pkgURI, string pkgPrefix, bool flag)   int

Enables or disables the given SBML Level 3 package on this object.

This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase.disablePackage().

Parameters
pkgURIthe URI of the package.
pkgPrefixthe XML prefix of the package
flagwhether to enable (True) or disable (False) the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
disablePackage()
def libsbml.SBase.getAncestorOfType (   self,
  args 
)
inherited

Python method signature(s):

getAncestorOfType(SBase self, int type, string pkgName="core")   SBase
getAncestorOfType(SBase self, int type)   SBase
getAncestorOfType(SBase self, int type, string pkgName="core")   SBase
getAncestorOfType(SBase self, int type)   SBase

Returns the first ancestor object that has the given SBML type code from the given package.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or None if no ancestor exists.
Warning
The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
def libsbml.SBase.getAnnotation (   self,
  args 
)
inherited

Python method signature(s):

getAnnotation(SBase self)   XMLNode
getAnnotation(SBase self)   XMLNode

Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.getAnnotationString (   self,
  args 
)
inherited

Python method signature(s):

getAnnotationString(SBase self)   string
getAnnotationString(SBase self)   string

Returns the content of the 'annotation' subelement of this object as a character string.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.

Returns
the annotation of this SBML object as a character string.
See also
getAnnotation()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.Model.getAreaUnits (   self)
inherited

Python method signature(s):

getAreaUnits(Model self)   string

Returns the value of the 'areaUnits' attribute of this Model.

Returns
the areaUnits of this Model.
Note
The 'areaUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.getAssignmentRule (   self,
  args 
)
inherited

Python method signature(s):

getAssignmentRule(Model self, string variable)   AssignmentRule
getAssignmentRule(Model self, string variable)   AssignmentRule

Get a Rule object based on the variable to which it assigns a value.

Returns
the Rule in this Model with the given 'variable' attribute value or None if no such Rule exists.
def libsbml.Model.getAssignmentRuleByVariable (   self,
  args 
)
inherited

Python method signature(s):

getAssignmentRuleByVariable(Model self, string variable)   AssignmentRule
getAssignmentRuleByVariable(Model self, string variable)   AssignmentRule

Get a Rule object based on the variable to which it assigns a value.

Returns
the Rule in this Model with the given 'variable' attribute value or None if no such Rule exists.
def libsbml.SBase.getColumn (   self)
inherited

Python method signature(s):

getColumn(SBase self)   long

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns
the column number of this SBML object.
Note
The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See also
getLine()
def libsbml.Model.getCompartment (   self,
  args 
)
inherited

Python method signature(s):

getCompartment(Model self, long n)   Compartment
getCompartment(Model self, long n)   Compartment
getCompartment(Model self, string sid)   Compartment
getCompartment(Model self, string sid)   Compartment

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getCompartment(long n)

Get the nth Compartment object in this Model.

Returns
the nth Compartment of this Model.

Method variant with the following signature:
getCompartment(string sid)

Get a Compartment object based on its identifier.

Returns
the Compartment in this Model with the identifier sid or None if no such Compartment exists.
def libsbml.Model.getCompartmentType (   self,
  args 
)
inherited

Python method signature(s):

getCompartmentType(Model self, long n)   CompartmentType
getCompartmentType(Model self, long n)   CompartmentType
getCompartmentType(Model self, string sid)   CompartmentType
getCompartmentType(Model self, string sid)   CompartmentType

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getCompartmentType(long n)

Get the nth CompartmentType object in this Model.

Returns
the nth CompartmentType of this Model.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

Method variant with the following signature:
getCompartmentType(string sid)

Get a CompartmentType object based on its identifier.

Returns
the CompartmentType in this Model with the identifier sid or None if no such CompartmentType exists.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
def libsbml.Model.getConstraint (   self,
  args 
)
inherited

Python method signature(s):

getConstraint(Model self, long n)   Constraint
getConstraint(Model self, long n)   Constraint

Get the nth Constraint object in this Model.

Returns
the nth Constraint of this Model.
def libsbml.Model.getConversionFactor (   self)
inherited

Python method signature(s):

getConversionFactor(Model self)   string

Returns the value of the 'conversionFactor' attribute of this Model.

Returns
the conversionFactor of this Model.
Note
The 'conversionFactor' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.SBase.getCVTerm (   self,
  args 
)
inherited

Python method signature(s):

getCVTerm(SBase self, long n)   CVTerm

Returns the nth CVTerm in the list of CVTerms of this SBML object.

Parameters
nlong the index of the CVTerm to retrieve
Returns
the nth CVTerm in the list of CVTerms for this SBML object.
def libsbml.SBase.getCVTerms (   self)
inherited

Python method signature(s):

getCVTerms()   CVTermList

Get the CVTermList of CVTerm objects in this SBase.

Returns the CVTermList for this SBase.

def libsbml.Model.getElementByMetaId (   self,
  args 
)
inherited

Python method signature(s):

getElementByMetaId(Model self, string metaid)   SBase

Returns the first child element it can find with the given metaid, or None if no such object is found.

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.
def libsbml.Model.getElementBySId (   self,
  args 
)
inherited

Python method signature(s):

getElementBySId(Model self, string id)   SBase

Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found.

Parameters
idstring representing the id of objects to find.
Returns
pointer to the first element found with the given id.
def libsbml.ModelDefinition.getElementName (   self)

Python method signature(s):

getElementName(ModelDefinition self)   string

The only difference between a Model and a ModelDefinition is the element name ('modelDefinition')

Returns
the string of the name of this element ('modelDefintion').
See also
getTypeCode()
def libsbml.Model.getEvent (   self,
  args 
)
inherited

Python method signature(s):

getEvent(Model self, long n)   Event
getEvent(Model self, long n)   Event
getEvent(Model self, string sid)   Event
getEvent(Model self, string sid)   Event

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getEvent(long n)

Get the nth Event object in this Model.

Returns
the nth Event of this Model.

Method variant with the following signature:
getEvent(string sid)

Get an Event object based on its identifier.

Returns
the Event in this Model with the identifier sid or None if no such Event exists.
def libsbml.Model.getExtentUnits (   self)
inherited

Python method signature(s):

getExtentUnits(Model self)   string

Returns the value of the 'extentUnits' attribute of this Model.

Returns
the extentUnits of this Model.
Note
The 'extentUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.getFunctionDefinition (   self,
  args 
)
inherited

Python method signature(s):

getFunctionDefinition(Model self, long n)   FunctionDefinition
getFunctionDefinition(Model self, long n)   FunctionDefinition
getFunctionDefinition(Model self, string sid)   FunctionDefinition
getFunctionDefinition(Model self, string sid)   FunctionDefinition

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getFunctionDefinition(long n)

Get the nth FunctionDefinitions object in this Model.

Returns
the nth FunctionDefinition of this Model.

Method variant with the following signature:
getFunctionDefinition(string sid)

Get a FunctionDefinition object based on its identifier.

Returns
the FunctionDefinition in this Model with the identifier sid or None if no such FunctionDefinition exists.
def libsbml.Model.getId (   self)
inherited

Python method signature(s):

getId(Model self)   string

Returns the value of the 'id' attribute of this Model.

Returns
the id of this Model.
def libsbml.Model.getInitialAssignment (   self,
  args 
)
inherited

Python method signature(s):

getInitialAssignment(Model self, long n)   InitialAssignment
getInitialAssignment(Model self, long n)   InitialAssignment
getInitialAssignment(Model self, string symbol)   InitialAssignment
getInitialAssignment(Model self, string symbol)   InitialAssignment

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getInitialAssignment(string symbol)

Get an InitialAssignment object based on the symbol to which it assigns a value.

Returns
the InitialAssignment in this Model with the given 'symbol' attribute value or None if no such InitialAssignment exists.

Method variant with the following signature:
getInitialAssignment(long n)

Get the nth InitialAssignment object in this Model.

Returns
the nth InitialAssignment of this Model.
def libsbml.Model.getInitialAssignmentBySymbol (   self,
  args 
)
inherited

Python method signature(s):

getInitialAssignmentBySymbol(Model self, string symbol)   InitialAssignment
getInitialAssignmentBySymbol(Model self, string symbol)   InitialAssignment

Get an InitialAssignment object based on the symbol to which it assigns a value.

Returns
the InitialAssignment in this Model with the given 'symbol' attribute value or None if no such InitialAssignment exists.
def libsbml.Model.getLengthUnits (   self)
inherited

Python method signature(s):

getLengthUnits(Model self)   string

Returns the value of the 'lengthUnits' attribute of this Model.

Returns
the lengthUnits of this Model.
Note
The 'lengthUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.SBase.getLevel (   self)
inherited

Python method signature(s):

getLevel(SBase self)   long

Returns the SBML Level of the SBMLDocument object containing this object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML level of this SBML object.
See also
getVersion()
getNamespaces()
getPackageVersion()
def libsbml.SBase.getLine (   self)
inherited

Python method signature(s):

getLine(SBase self)   long

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns
the line number of this SBML object.
Note
The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See also
getColumn()
def libsbml.SBase.getListOfAllElements (   self,
  filter = None 
)
inherited

Python method signature(s):

getListOfAllElements(SBase self, ElementFilter filter=None)   SBaseList
getListOfAllElements(SBase self)   SBaseList

Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.

Returns
an SBaseList
def libsbml.SBase.getListOfAllElementsFromPlugins (   self,
  filter = None 
)
inherited

Python method signature(s):

getListOfAllElementsFromPlugins(SBase self, ElementFilter filter=None)   SBaseList
getListOfAllElementsFromPlugins(SBase self)   SBaseList

Returns an SBaseList of all child SBase objects contained in SBML package plugins.

This method walks down the list of all packages used by the model and returns all objects contained in them.

Returns
an SBaseList of all children objects from plugins.
def libsbml.Model.getListOfCompartments (   self,
  args 
)
inherited

Python method signature(s):

getListOfCompartments(Model self)   ListOfCompartments
getListOfCompartments(Model self)   ListOfCompartments

Get the ListOfCompartments object in this Model.

Returns
the list of Compartments for this Model.
def libsbml.Model.getListOfCompartmentTypes (   self,
  args 
)
inherited

Python method signature(s):

getListOfCompartmentTypes(Model self)   ListOfCompartmentTypes
getListOfCompartmentTypes(Model self)   ListOfCompartmentTypes

Get the ListOfCompartmentTypes object in this Model.

Returns
the list of CompartmentTypes for this Model.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
def libsbml.Model.getListOfConstraints (   self,
  args 
)
inherited

Python method signature(s):

getListOfConstraints(Model self)   ListOfConstraints
getListOfConstraints(Model self)   ListOfConstraints

Get the ListOfConstraints object in this Model.

Returns
the list of Constraints for this Model.
def libsbml.Model.getListOfEvents (   self,
  args 
)
inherited

Python method signature(s):

getListOfEvents(Model self)   ListOfEvents
getListOfEvents(Model self)   ListOfEvents

Get the ListOfEvents object in this Model.

Returns
the list of Events for this Model.
def libsbml.Model.getListOfFunctionDefinitions (   self,
  args 
)
inherited

Python method signature(s):

getListOfFunctionDefinitions(Model self)   ListOfFunctionDefinitions
getListOfFunctionDefinitions(Model self)   ListOfFunctionDefinitions

Get the ListOfFunctionDefinitions object in this Model.

Returns
the list of FunctionDefinitions for this Model.
def libsbml.Model.getListOfInitialAssignments (   self,
  args 
)
inherited

Python method signature(s):

getListOfInitialAssignments(Model self)   ListOfInitialAssignments
getListOfInitialAssignments(Model self)   ListOfInitialAssignments

Get the ListOfInitialAssignments object in this Model.

Returns
the list of InitialAssignments for this Model.
def libsbml.Model.getListOfParameters (   self,
  args 
)
inherited

Python method signature(s):

getListOfParameters(Model self)   ListOfParameters
getListOfParameters(Model self)   ListOfParameters

Get the ListOfParameters object in this Model.

Returns
the list of Parameters for this Model.
def libsbml.Model.getListOfReactions (   self,
  args 
)
inherited

Python method signature(s):

getListOfReactions(Model self)   ListOfReactions
getListOfReactions(Model self)   ListOfReactions

Get the ListOfReactions object in this Model.

Returns
the list of Reactions for this Model.
def libsbml.Model.getListOfRules (   self,
  args 
)
inherited

Python method signature(s):

getListOfRules(Model self)   ListOfRules
getListOfRules(Model self)   ListOfRules

Get the ListOfRules object in this Model.

Returns
the list of Rules for this Model.
def libsbml.Model.getListOfSpecies (   self,
  args 
)
inherited

Python method signature(s):

getListOfSpecies(Model self)   ListOfSpecies
getListOfSpecies(Model self)   ListOfSpecies

Get the ListOfSpecies object in this Model.

Returns
the list of Species for this Model.
def libsbml.Model.getListOfSpeciesTypes (   self,
  args 
)
inherited

Python method signature(s):

getListOfSpeciesTypes(Model self)   ListOfSpeciesTypes
getListOfSpeciesTypes(Model self)   ListOfSpeciesTypes

Get the ListOfSpeciesTypes object in this Model.

Returns
the list of SpeciesTypes for this Model.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
def libsbml.Model.getListOfUnitDefinitions (   self,
  args 
)
inherited

Python method signature(s):

getListOfUnitDefinitions(Model self)   ListOfUnitDefinitions
getListOfUnitDefinitions(Model self)   ListOfUnitDefinitions

Get the ListOfUnitDefinitions object in this Model.

Returns
the list of UnitDefinitions for this Model.
def libsbml.SBase.getMetaId (   self)
inherited

Python method signature(s):

getMetaId(SBase self)   string

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
the meta-identifier of this SBML object.
See also
isSetMetaId()
setMetaId()
def libsbml.SBase.getModel (   self)
inherited

Python method signature(s):

getModel(SBase self)   Model

Returns the Model object for the SBML Document in which the current object is located.

Returns
the Model object for the SBML Document of this SBML object.
See also
getParentSBMLObject()
getSBMLDocument()
def libsbml.SBase.getModelHistory (   self,
  args 
)
inherited

Python method signature(s):

getModelHistory(SBase self)   ModelHistory
getModelHistory(SBase self)   ModelHistory

Returns the ModelHistory object, if any, attached to this object.

Returns
the ModelHistory object attached to this object, or None if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.Model.getModifierSpeciesReference (   self,
  args 
)
inherited

Python method signature(s):

getModifierSpeciesReference(Model self, string sid)   ModifierSpeciesReference
getModifierSpeciesReference(Model self, string sid)   ModifierSpeciesReference

Get a ModifierSpeciesReference object based on its identifier.

Returns
the ModifierSpeciesReference in this Model with the identifier sid or None if no such ModifierSpeciesReference exists.
def libsbml.Model.getName (   self)
inherited

Python method signature(s):

getName(Model self)   string

Returns the value of the 'name' attribute of this Model.

Returns
the name of this Model.
def libsbml.SBase.getNamespaces (   self)
inherited

Python method signature(s):

getNamespaces(SBase self)   XMLNamespaces

Returns a list of the XML Namespaces declared on this SBML document.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Returns
the XML Namespaces associated with this SBML object, or None in certain very usual circumstances where a namespace is not set.
See also
getLevel()
getVersion()
def libsbml.SBase.getNotes (   self,
  args 
)
inherited

Python method signature(s):

getNotes(SBase self)   XMLNode
getNotes(SBase self)   XMLNode

Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.

The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().

Returns
the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.getNotesString (   self,
  args 
)
inherited

Python method signature(s):

getNotesString(SBase self)   string
getNotesString(SBase self)   string

Returns the content of the 'notes' subelement of this object as a string.

The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.

Returns
the content of the 'notes' subelement of this SBML object as a string.
See also
getNotes()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.Model.getNumCompartments (   self)
inherited

Python method signature(s):

getNumCompartments(Model self)   long

Get the number of Compartment objects in this Model.

Returns
the number of Compartments in this Model.
def libsbml.Model.getNumCompartmentTypes (   self)
inherited

Python method signature(s):

getNumCompartmentTypes(Model self)   long

Get the number of CompartmentType objects in this Model.

Returns
the number of CompartmentTypes in this Model.
Note
The CompartmentType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
def libsbml.Model.getNumConstraints (   self)
inherited

Python method signature(s):

getNumConstraints(Model self)   long

Get the number of Constraint objects in this Model.

Returns
the number of Constraints in this Model.
def libsbml.SBase.getNumCVTerms (   self)
inherited

Python method signature(s):

getNumCVTerms(SBase self)   long

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns
the number of CVTerms for this SBML object.
def libsbml.Model.getNumEvents (   self)
inherited

Python method signature(s):

getNumEvents(Model self)   long

Get the number of Event objects in this Model.

Returns
the number of Events in this Model.
def libsbml.Model.getNumFunctionDefinitions (   self)
inherited

Python method signature(s):

getNumFunctionDefinitions(Model self)   long

Get the number of FunctionDefinition objects in this Model.

Returns
the number of FunctionDefinitions in this Model.
def libsbml.Model.getNumInitialAssignments (   self)
inherited

Python method signature(s):

getNumInitialAssignments(Model self)   long

Get the number of InitialAssignment objects in this Model.

Returns
the number of InitialAssignments in this Model.
def libsbml.Model.getNumParameters (   self)
inherited

Python method signature(s):

getNumParameters(Model self)   long

Get the number of Parameter objects in this Model.

Returns
the number of Parameters in this Model. Parameters defined in KineticLaws are not included.
def libsbml.SBase.getNumPlugins (   self)
inherited

Python method signature(s):

getNumPlugins(SBase self)   long

Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
def libsbml.Model.getNumReactions (   self)
inherited

Python method signature(s):

getNumReactions(Model self)   long

Get the number of Reaction objects in this Model.

Returns
the number of Reactions in this Model.
def libsbml.Model.getNumRules (   self)
inherited

Python method signature(s):

getNumRules(Model self)   long

Get the number of Rule objects in this Model.

Returns
the number of Rules in this Model.
def libsbml.Model.getNumSpecies (   self)
inherited

Python method signature(s):

getNumSpecies(Model self)   long

Get the number of Specie objects in this Model.

Returns
the number of Species in this Model.
def libsbml.Model.getNumSpeciesTypes (   self)
inherited

Python method signature(s):

getNumSpeciesTypes(Model self)   long

Get the number of SpeciesType objects in this Model.

Returns
the number of SpeciesTypes in this Model.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
def libsbml.Model.getNumSpeciesWithBoundaryCondition (   self)
inherited

Python method signature(s):

getNumSpeciesWithBoundaryCondition(Model self)   long

Get the number of Species in this Model having their 'boundaryCondition' attribute value set to True.

Returns
the number of Species in this Model with boundaryCondition set to true.
def libsbml.Model.getNumUnitDefinitions (   self)
inherited

Python method signature(s):

getNumUnitDefinitions(Model self)   long

Get the number of UnitDefinition objects in this Model.

Returns
the number of UnitDefinitions in this Model.
def libsbml.SBase.getPackageName (   self)
inherited

Python method signature(s):

getPackageName(SBase self)   string

Returns the name of the SBML Level 3 package in which this element is defined.

Returns
the name of the SBML package in which this element is defined. The string "core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.
def libsbml.SBase.getPackageVersion (   self)
inherited

Python method signature(s):

getPackageVersion(SBase self)   long

Returns the Version of the SBML Level 3 package to which this element belongs to.

Returns
the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.
See also
getLevel()
getVersion()
def libsbml.Model.getParameter (   self,
  args 
)
inherited

Python method signature(s):

getParameter(Model self, long n)   Parameter
getParameter(Model self, long n)   Parameter
getParameter(Model self, string sid)   Parameter
getParameter(Model self, string sid)   Parameter

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getParameter(long n)

Get the nth Parameter object in this Model.

Returns
the nth Parameter of this Model.

Method variant with the following signature:
getParameter(string sid)

Get a Parameter object based on its identifier.

Returns
the Parameter in this Model with the identifier sid or None if no such Parameter exists.
def libsbml.SBase.getParentSBMLObject (   self,
  args 
)
inherited

Python method signature(s):

getParentSBMLObject(SBase self)   SBase
getParentSBMLObject(SBase self)   SBase

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns
the parent SBML object of this SBML object.
See also
getSBMLDocument()
getModel()
def libsbml.SBase.getPlugin (   self,
  args 
)
inherited

Python method signature(s):

getPlugin(SBase self, string package)   SBasePlugin
getPlugin(SBase self, string package)   SBasePlugin
getPlugin(SBase self, long n)   SBasePlugin
getPlugin(SBase self, long n)   SBasePlugin

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getPlugin(long n)

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
nthe index of the plug-in to return
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.

Method variant with the following signature:
getPlugin(string package)

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
packagethe name or URI of the package
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
def libsbml.SBase.getPrefix (   self)
inherited

Python method signature(s):

getPrefix(SBase self)   string

Returns the namespace prefix of this element.

def libsbml.Model.getRateRule (   self,
  args 
)
inherited

Python method signature(s):

getRateRule(Model self, string variable)   RateRule
getRateRule(Model self, string variable)   RateRule

Get a Rule object based on the variable to which it assigns a value.

Returns
the Rule in this Model with the given 'variable' attribute value or None if no such Rule exists.
def libsbml.Model.getRateRuleByVariable (   self,
  args 
)
inherited

Python method signature(s):

getRateRuleByVariable(Model self, string variable)   RateRule
getRateRuleByVariable(Model self, string variable)   RateRule

Get a Rule object based on the variable to which it assigns a value.

Returns
the Rule in this Model with the given 'variable' attribute value or None if no such Rule exists.
def libsbml.Model.getReaction (   self,
  args 
)
inherited

Python method signature(s):

getReaction(Model self, long n)   Reaction
getReaction(Model self, long n)   Reaction
getReaction(Model self, string sid)   Reaction
getReaction(Model self, string sid)   Reaction

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getReaction(long n)

Get the nth Reaction object in this Model.

Returns
the nth Reaction of this Model.

Method variant with the following signature:
getReaction(string sid)

Get a Reaction object based on its identifier.

Returns
the Reaction in this Model with the identifier sid or None if no such Reaction exists.
def libsbml.SBase.getResourceBiologicalQualifier (   self,
  args 
)
inherited

Python method signature(s):

getResourceBiologicalQualifier(SBase self, string resource)   long

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose name begins with BQB_ from the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
def libsbml.SBase.getResourceModelQualifier (   self,
  args 
)
inherited

Python method signature(s):

getResourceModelQualifier(SBase self, string resource)   long

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQM_ in the interface class libsbml.

This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose name begins with BQM_ from the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the model qualifier type associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
def libsbml.Model.getRule (   self,
  args 
)
inherited

Python method signature(s):

getRule(Model self, long n)   Rule
getRule(Model self, long n)   Rule
getRule(Model self, string variable)   Rule
getRule(Model self, string variable)   Rule

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getRule(string variable)

Get a Rule object based on the variable to which it assigns a value.

Returns
the Rule in this Model with the given 'variable' attribute value or None if no such Rule exists.

Method variant with the following signature:
getRule(long n)

Get the nth Rule object in this Model.

Returns
the nth Rule of this Model.
def libsbml.Model.getRuleByVariable (   self,
  args 
)
inherited

Python method signature(s):

getRuleByVariable(Model self, string variable)   Rule
getRuleByVariable(Model self, string variable)   Rule

Get a Rule object based on the variable to which it assigns a value.

Returns
the Rule in this Model with the given 'variable' attribute value or None if no such Rule exists.
def libsbml.SBase.getSBMLDocument (   self,
  args 
)
inherited

Python method signature(s):

getSBMLDocument(SBase self)   SBMLDocument
getSBMLDocument(SBase self)   SBMLDocument

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this SBML object.
See also
getParentSBMLObject()
getModel()
def libsbml.SBase.getSBOTerm (   self)
inherited

Python method signature(s):

getSBOTerm(SBase self)   int

Returns the integer portion of the value of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as an integer, or -1 if the value is not set.
def libsbml.SBase.getSBOTermAsURL (   self)
inherited

Python method signature(s):

getSBOTermAsURL(SBase self)   string

Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.

This method returns the entire SBO identifier as a text string in the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as an identifiers.org URL (its value will be of the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'), or an empty string if the value is not set.
def libsbml.SBase.getSBOTermID (   self)
inherited

Python method signature(s):

getSBOTermID(SBase self)   string

Returns the string representation of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as a string (its value will be of the form 'SBO:NNNNNNN'), or an empty string if the value is not set.
def libsbml.Model.getSpecies (   self,
  args 
)
inherited

Python method signature(s):

getSpecies(Model self, long n)   Species
getSpecies(Model self, long n)   Species
getSpecies(Model self, string sid)   Species
getSpecies(Model self, string sid)   Species

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getSpecies(long n)

Get the nth Species object in this Model.

Returns
the nth Species of this Model.

Method variant with the following signature:
getSpecies(string sid)

Get a Species object based on its identifier.

Returns
the Species in this Model with the identifier sid or None if no such Species exists.
def libsbml.Model.getSpeciesReference (   self,
  args 
)
inherited

Python method signature(s):

getSpeciesReference(Model self, string sid)   SpeciesReference
getSpeciesReference(Model self, string sid)   SpeciesReference

Get a SpeciesReference object based on its identifier.

Returns
the SpeciesReference in this Model with the identifier sid or None if no such SpeciesReference exists.
def libsbml.Model.getSpeciesType (   self,
  args 
)
inherited

Python method signature(s):

getSpeciesType(Model self, long n)   SpeciesType
getSpeciesType(Model self, long n)   SpeciesType
getSpeciesType(Model self, string sid)   SpeciesType
getSpeciesType(Model self, string sid)   SpeciesType

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getSpeciesType(long n)

Get the nth SpeciesType object in this Model.

Returns
the nth SpeciesType of this Model.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.

Method variant with the following signature:
getSpeciesType(string sid)

Get a SpeciesType object based on its identifier.

Returns
the SpeciesType in this Model with the identifier sid or None if no such SpeciesType exists.
Note
The SpeciesType object class is only available in SBML Level 2 Versions 2–4. It is not available in Level 1 nor Level 3.
def libsbml.Model.getSubstanceUnits (   self)
inherited

Python method signature(s):

getSubstanceUnits(Model self)   string

Returns the value of the 'substanceUnits' attribute of this Model.

Returns
the substanceUnits of this Model.
Note
The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.getTimeUnits (   self)
inherited

Python method signature(s):

getTimeUnits(Model self)   string

Returns the value of the 'timeUnits' attribute of this Model.

Returns
the timeUnits of this Model.
Note
The 'timeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.ModelDefinition.getTypeCode (   self)

Python method signature(s):

getTypeCode(ModelDefinition self)   int

Returns the libSBML type code of this object instance.

LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters “SBML_”. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the getPackageName() method on the object.
Returns
the SBML type code for this object: SBML_COMP_MODELDEFINITION
Warning
The specific integer values of the possible type codes may be reused by different Level 3 package plug-ins. Thus, to identifiy the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
See also
getElementName()
getPackageName()
def libsbml.Model.getUnitDefinition (   self,
  args 
)
inherited

Python method signature(s):

getUnitDefinition(Model self, long n)   UnitDefinition
getUnitDefinition(Model self, long n)   UnitDefinition
getUnitDefinition(Model self, string sid)   UnitDefinition
getUnitDefinition(Model self, string sid)   UnitDefinition

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getUnitDefinition(long n)

Get the nth UnitDefinition object in this Model.

Returns
the nth UnitDefinition of this Model.

Method variant with the following signature:
getUnitDefinition(string sid)

Get a UnitDefinition based on its identifier.

Returns
the UnitDefinition in this Model with the identifier sid or None if no such UnitDefinition exists.
def libsbml.SBase.getURI (   self)
inherited

Python method signature(s):

getURI(SBase self)   string

Gets the namespace URI to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it willreturn the XML namespace to which this element belongs.

Returns
the URI of this element
See also
getSBMLDocument()
getPackageName()
def libsbml.SBase.getVersion (   self)
inherited

Python method signature(s):

getVersion(SBase self)   long

Returns the Version within the SBML Level of the SBMLDocument object containing this object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML version of this SBML object.
See also
getLevel()
getNamespaces()
def libsbml.Model.getVolumeUnits (   self)
inherited

Python method signature(s):

getVolumeUnits(Model self)   string

Returns the value of the 'volumeUnits' attribute of this Model.

Returns
the volumeUnits of this Model.
Note
The 'volumeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.hasRequiredElements (   self)
inherited

Python method signature(s):

hasRequiredElements(Model self)   bool

Predicate returning True if all the required elements for this Model object have been set.

Note
The required elements for a Model object are: listOfCompartments (L1 only); listOfSpecies (L1V1 only); listOfReactions(L1V1 only)
Returns
a boolean value indicating whether all the required elements for this object have been defined.
def libsbml.SBase.hasValidLevelVersionNamespaceCombination (   self)
inherited

Python method signature(s):

hasValidLevelVersionNamespaceCombination(SBase self)   bool
def libsbml.SBase.isPackageEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPackageEnabled(SBase self, string pkgName)   bool

Predicate returning True if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPackageURIEnabled()
def libsbml.SBase.isPackageURIEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPackageURIEnabled(SBase self, string pkgURI)   bool

Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPackageEnabled()
def libsbml.SBase.isPkgEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPkgEnabled(SBase self, string pkgName)   bool

Predicate returning True if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPkgURIEnabled()
def libsbml.SBase.isPkgURIEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPkgURIEnabled(SBase self, string pkgURI)   bool

Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPkgEnabled()
def libsbml.Model.isPopulatedListFormulaUnitsData (   self)
inherited

Python method signature(s):

isPopulatedListFormulaUnitsData(Model self)   bool

Predicate returning True if the list of FormulaUnitsData is populated.

Returns
True if the list of FormulaUnitsData is populated, False otherwise.
def libsbml.SBase.isSetAnnotation (   self)
inherited

Python method signature(s):

isSetAnnotation(SBase self)   bool

Predicate returning True if this object's 'annotation' subelement exists and has content.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
True if a 'annotation' subelement exists, False otherwise.
See also
getAnnotation()
getAnnotationString()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.Model.isSetAreaUnits (   self)
inherited

Python method signature(s):

isSetAreaUnits(Model self)   bool

Predicate returning True if this Model's 'areaUnits' attribute is set.

Returns
True if the 'areaUnits' attribute of this Model is set, False otherwise.
Note
The 'areaUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.isSetConversionFactor (   self)
inherited

Python method signature(s):

isSetConversionFactor(Model self)   bool

Predicate returning True if this Model's 'conversionFactor' attribute is set.

Returns
True if the 'conversionFactor' attribute of this Model is set, False otherwise.
Note
The 'conversionFactor' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.isSetExtentUnits (   self)
inherited

Python method signature(s):

isSetExtentUnits(Model self)   bool

Predicate returning True if this Model's 'extentUnits' attribute is set.

Returns
True if the 'extentUnits' attribute of this Model is set, False otherwise.
Note
The 'extentUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.isSetId (   self)
inherited

Python method signature(s):

isSetId(Model self)   bool

Predicate returning True if this Model's 'id' attribute is set.

Returns
True if the 'id' attribute of this Model is set, False otherwise.
def libsbml.Model.isSetLengthUnits (   self)
inherited

Python method signature(s):

isSetLengthUnits(Model self)   bool

Predicate returning True if this Model's 'lengthUnits' attribute is set.

Returns
True if the 'lengthUnits' attribute of this Model is set, False otherwise.
Note
The 'lengthUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.SBase.isSetMetaId (   self)
inherited

Python method signature(s):

isSetMetaId(SBase self)   bool

Predicate returning True if this object's 'metaid' attribute is set.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
True if the 'metaid' attribute of this SBML object is set, False otherwise.
See also
getMetaId()
setMetaId()
def libsbml.SBase.isSetModelHistory (   self)
inherited

Python method signature(s):

isSetModelHistory(SBase self)   bool

Predicate returning True if this object has a ModelHistory object attached to it.

Returns
True if the ModelHistory of this object is set, false otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.Model.isSetName (   self)
inherited

Python method signature(s):

isSetName(Model self)   bool

Predicate returning True if this Model's 'name' attribute is set.

Returns
True if the 'name' attribute of this Model is set, False otherwise.
def libsbml.SBase.isSetNotes (   self)
inherited

Python method signature(s):

isSetNotes(SBase self)   bool

Predicate returning True if this object's 'notes' subelement exists and has content.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
True if a 'notes' subelement exists, False otherwise.
See also
getNotes()
getNotesString()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.isSetSBOTerm (   self)
inherited

Python method signature(s):

isSetSBOTerm(SBase self)   bool

Predicate returning True if this object's 'sboTerm' attribute is set.

Returns
True if the 'sboTerm' attribute of this SBML object is set, False otherwise.
def libsbml.Model.isSetSubstanceUnits (   self)
inherited

Python method signature(s):

isSetSubstanceUnits(Model self)   bool

Predicate returning True if this Model's 'substanceUnits' attribute is set.

Returns
True if the 'substanceUnits' attribute of this Model is set, False otherwise.
Note
The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.isSetTimeUnits (   self)
inherited

Python method signature(s):

isSetTimeUnits(Model self)   bool

Predicate returning True if this Model's 'timeUnits' attribute is set.

Returns
True if the 'timeUnits' attribute of this Model is set, False otherwise.
Note
The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.isSetVolumeUnits (   self)
inherited

Python method signature(s):

isSetVolumeUnits(Model self)   bool

Predicate returning True if this Model's 'volumeUnits' attribute is set.

Returns
True if the 'volumeUnits' attribute of this Model is set, False otherwise.
Note
The 'volumeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.SBase.matchesRequiredSBMLNamespacesForAddition (   self,
  args 
)
inherited

Python method signature(s):

matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)   bool
matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)   bool

Returns True if this object's set of XML namespaces are a subset of the given object's XML namespaces.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces
Returns
boolean, True if this object's collection of namespaces is a subset of sb's, False otherwise.
def libsbml.SBase.matchesSBMLNamespaces (   self,
  args 
)
inherited

Python method signature(s):

matchesSBMLNamespaces(SBase self, SBase sb)   bool
matchesSBMLNamespaces(SBase self, SBase sb)   bool

Returns True if this object's set of XML namespaces are the same as the given object's XML namespaces.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces
Returns
boolean, True if this object's collection of namespaces is the same as sb's, False otherwise.
def libsbml.Model.populateListFormulaUnitsData (   self)
inherited

Python method signature(s):

populateListFormulaUnitsData(Model self)

Populates the list of FormulaDataUnits with the units derived for the model. The list contains elements of class FormulaUnitsData.

The first element of the list refers to the default units of 'substance per time' derived from the model and has the unitReferenceId 'subs_per_time'. This facilitates the comparison of units derived from mathematical formula with the expected units.

The next elements of the list record the units of the compartments and species established from either explicitly declared or default units.

The next elements record the units of any parameters.

Subsequent elements of the list record the units derived for each mathematical expression encountered within the model.

Note
This function is utilised by the Unit Consistency Validator. The list is populated prior to running the validation and thus the consistency of units can be checked by accessing the members of the list and comparing the appropriate data.
def libsbml.Model.removeCompartment (   self,
  args 
)
inherited

Python method signature(s):

removeCompartment(Model self, long n)   Compartment
removeCompartment(Model self, string sid)   Compartment

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeCompartment(long n)

Removes the nth Compartment object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Compartment object to remove
Returns
the Compartment object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:
removeCompartment(string sid)

Removes the Compartment object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the Compartment objects in this Model object have the identifier sid, then None is returned.

Parameters
sidthe identifier of the Compartment object to remove
Returns
the Compartment object removed. As mentioned above, the caller owns the returned object. None is returned if no Compartment object with the identifier exists in this Model object.
def libsbml.Model.removeCompartmentType (   self,
  args 
)
inherited

Python method signature(s):

removeCompartmentType(Model self, long n)   CompartmentType
removeCompartmentType(Model self, string sid)   CompartmentType

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeCompartmentType(long n)

Removes the nth CompartmentType object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the CompartmentType object to remove
Returns
the ComapartmentType object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:
removeCompartmentType(string sid)

Removes the CompartmentType object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the CompartmentType objects in this Model object have the identifier sid, then None is returned.

Parameters
sidthe identifier of the object to remove
Returns
the CompartmentType object removed. As mentioned above, the caller owns the returned object. None is returned if no CompartmentType object with the identifier exists in this Model object.
def libsbml.Model.removeConstraint (   self,
  args 
)
inherited

Python method signature(s):

removeConstraint(Model self, long n)   Constraint

Removes the nth Constraint object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Constraint object to remove
Returns
the Constraint object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.
def libsbml.Model.removeEvent (   self,
  args 
)
inherited

Python method signature(s):

removeEvent(Model self, long n)   Event
removeEvent(Model self, string sid)   Event

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeEvent(long n)

Removes the nth Event object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Event object to remove
Returns
the Event object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:
removeEvent(string sid)

Removes the Event object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the Event objects in this Model object have the identifier sid, then None is returned.

Parameters
sidthe identifier of the Event object to remove
Returns
the Event object removed. As mentioned above, the caller owns the returned object. None is returned if no Event object with the identifier exists in this Model object.
def libsbml.ModelDefinition.removeFromParentAndDelete (   self)

Python method signature(s):

removeFromParentAndDelete(ModelDefinition self)   int

Finds this Model's parent ListOfModelDefinitions and removes itself from it and deletes itself.

This method actually just calls the SBase function, since the Model class overrides it, but that's actually what we want to happen here.

Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.Model.removeFunctionDefinition (   self,
  args 
)
inherited

Python method signature(s):

removeFunctionDefinition(Model self, long n)   FunctionDefinition
removeFunctionDefinition(Model self, string sid)   FunctionDefinition

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeFunctionDefinition(long n)

Removes the nth FunctionDefinition object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the FunctionDefinition object to remove
Returns
the FunctionDefinition object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:
removeFunctionDefinition(string sid)

Removes the FunctionDefinition object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the FunctionDefinition objects in this Model object have the identifier sid, then None is returned.

Parameters
sidthe identifier of the FunctionDefinition object to remove
Returns
the FunctionDefinition object removed. As mentioned above, the caller owns the returned object. None is returned if no FunctionDefinition object with the identifier exists in this Model object.
def libsbml.Model.removeInitialAssignment (   self,
  args 
)
inherited

Python method signature(s):

removeInitialAssignment(Model self, long n)   InitialAssignment
removeInitialAssignment(Model self, string symbol)   InitialAssignment

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeInitialAssignment(string symbol)

Removes the InitialAssignment object with the given 'symbol' attribute from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the InitialAssignment objects in this Model object have the 'symbol' attribute symbol, then None is returned.

Parameters
symbolthe 'symbol' attribute of the InitialAssignment object to remove
Returns
the InitialAssignment object removed. As mentioned above, the caller owns the returned object. None is returned if no InitialAssignment object with the 'symbol' attribute exists in this Model object.

Method variant with the following signature:
removeInitialAssignment(long n)

Removes the nth InitialAssignment object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the InitialAssignment object to remove
Returns
the InitialAssignment object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.
def libsbml.Model.removeParameter (   self,
  args 
)
inherited

Python method signature(s):

removeParameter(Model self, long n)   Parameter
removeParameter(Model self, string sid)   Parameter

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeParameter(long n)

Removes the nth Parameter object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Parameter object to remove
Returns
the Parameter object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:
removeParameter(string sid)

Removes the Parameter object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the Parameter objects in this Model object have the identifier sid, then None is returned.

Parameters
sidthe identifier of the Parameter object to remove
Returns
the Parameter object removed. As mentioned above, the caller owns the returned object. None is returned if no Parameter object with the identifier exists in this Model object.
def libsbml.Model.removeReaction (   self,
  args 
)
inherited

Python method signature(s):

removeReaction(Model self, long n)   Reaction
removeReaction(Model self, string sid)   Reaction

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeReaction(long n)

Removes the nth Reaction object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Reaction object to remove
Returns
the Reaction object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:
removeReaction(string sid)

Removes the Reaction object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the Reaction objects in this Model object have the identifier sid, then None is returned.

Parameters
sidthe identifier of the Reaction object to remove
Returns
the Reaction object removed. As mentioned above, the caller owns the returned object. None is returned if no Reaction object with the identifier exists in this Model object.
def libsbml.Model.removeRule (   self,
  args 
)
inherited

Python method signature(s):

removeRule(Model self, long n)   Rule
removeRule(Model self, string variable)   Rule

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeRule(string variable)

Removes the Rule object with the given 'variable' attribute from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the Rule objects in this Model object have the 'variable' attribute variable, then None is returned.

Parameters
variablethe 'variable' attribute of the Rule object to remove
Returns
the Rule object removed. As mentioned above, the caller owns the returned object. None is returned if no Rule object with the 'variable' attribute exists in this Model object.

Method variant with the following signature:
removeRule(long n)

Removes the nth Rule object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Rule object to remove
Returns
the Rule object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.
def libsbml.Model.removeSpecies (   self,
  args 
)
inherited

Python method signature(s):

removeSpecies(Model self, long n)   Species
removeSpecies(Model self, string sid)   Species

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeSpecies(long n)

Removes the nth Species object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Species object to remove
Returns
the Species object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:
removeSpecies(string sid)

Removes the Species object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the Species objects in this Model object have the identifier sid, then None is returned.

Parameters
sidthe identifier of the Species object to remove
Returns
the Species object removed. As mentioned above, the caller owns the returned object. None is returned if no Species object with the identifier exists in this Model object.
def libsbml.Model.removeSpeciesType (   self,
  args 
)
inherited

Python method signature(s):

removeSpeciesType(Model self, long n)   SpeciesType
removeSpeciesType(Model self, string sid)   SpeciesType

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeSpeciesType(long n)

Removes the nth SpeciesType object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the SpeciesType object to remove
Returns
the SpeciesType object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:
removeSpeciesType(string sid)

Removes the SpeciesType object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the SpeciesType objects in this Model object have the identifier sid, then None is returned.

Parameters
sidthe identifier of the SpeciesType object to remove
Returns
the SpeciesType object removed. As mentioned above, the caller owns the returned object. None is returned if no SpeciesType object with the identifier exists in this Model object.
def libsbml.SBase.removeTopLevelAnnotationElement (   self,
  args 
)
inherited

Python method signature(s):

removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="", bool removeEmpty=True)   int
removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="")   int
removeTopLevelAnnotationElement(SBase self, string elementName)   int

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
removeEmptyif after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
replaceTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()
def libsbml.Model.removeUnitDefinition (   self,
  args 
)
inherited

Python method signature(s):

removeUnitDefinition(Model self, long n)   UnitDefinition
removeUnitDefinition(Model self, string sid)   UnitDefinition

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeUnitDefinition(long n)

Removes the nth UnitDefinition object from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the UnitDefinition object to remove
Returns
the UnitDefinition object removed. As mentioned above, the caller owns the returned item. None is returned if the given index is out of range.

Method variant with the following signature:
removeUnitDefinition(string sid)

Removes the UnitDefinition object with the given identifier from this Model object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it. If none of the UnitDefinition objects in this Model object have the identifier sid, then None is returned.

Parameters
sidthe identifier of the UnitDefinition object to remove
Returns
the UnitDefinition object removed. As mentioned above, the caller owns the returned object. None is returned if no UnitDefinition object with the identifier exists in this Model object.
def libsbml.Model.renameIDs (   self,
  args 
)
inherited

Python method signature(s):

renameIDs(Model self, SBaseList elements, IdentifierTransformer idTransformer)
 
def libsbml.SBase.renameMetaIdRefs (   self,
  args 
)
inherited

Python method signature(s):

renameMetaIdRefs(SBase self, string oldid, string newid)

Renames all the meta-identifier attributes on this element.

In SBML, object 'meta' identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as 'metaid refs', in analogy to the SBML-defined type SIdRef.

This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.Model.renameSIdRefs (   self,
  args 
)
inherited

Python method signature(s):

renameSIdRefs(Model self, string oldid, string newid)

Renames all the SIdRef attributes on this element, including any found in MathML.

In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to an identifier', but the effective data type was the same as SIdRefin Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all attributes and (if appropriate) mathematical formulas, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.Model.renameUnitSIdRefs (   self,
  args 
)
inherited

Python method signature(s):

renameUnitSIdRefs(Model self, string oldid, string newid)

Renames all the UnitSIdRef attributes on this element.

In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the unit identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.SBase.replaceTopLevelAnnotationElement (   self,
  args 
)
inherited

Python method signature(s):

replaceTopLevelAnnotationElement(SBase self, XMLNode annotation)   int
replaceTopLevelAnnotationElement(SBase self, string annotation)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
replaceTopLevelAnnotationElement(XMLNode annotation)

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.

Parameters
annotationXMLNode representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()

Method variant with the following signature:
replaceTopLevelAnnotationElement(string annotation)

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.

Parameters
annotationstring representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()
def libsbml.Model.setAnnotation (   self,
  args 
)
inherited

Python method signature(s):

setAnnotation(Model self, XMLNode annotation)   int
setAnnotation(Model self, string annotation)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
setAnnotation(XMLNode annotation)

Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.

Any existing content of the 'annotation' subelement is discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use appendAnnotation().

Parameters
annotationan XML structure that is to be used as the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
appendAnnotation()

Method variant with the following signature:
setAnnotation(string annotation)

Sets the value of the 'annotation' subelement of this SBML object to a copy of annotation.

Any existing content of the 'annotation' subelement is discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use appendAnnotation().

Parameters
annotationan XML string that is to be used as the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
appendAnnotation()
def libsbml.Model.setAreaUnits (   self,
  args 
)
inherited

Python method signature(s):

setAreaUnits(Model self, string units)   int

Sets the value of the 'areaUnits' attribute of this Model.

The string in units is copied.

Parameters
unitsthe new areaUnits for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'areaUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.setConversionFactor (   self,
  args 
)
inherited

Python method signature(s):

setConversionFactor(Model self, string units)   int

Sets the value of the 'conversionFactor' attribute of this Model.

The string in units is copied.

Parameters
unitsthe new conversionFactor for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'conversionFactor' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.setExtentUnits (   self,
  args 
)
inherited

Python method signature(s):

setExtentUnits(Model self, string units)   int

Sets the value of the 'extentUnits' attribute of this Model.

The string in units is copied.

Parameters
unitsthe new extentUnits for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'extentUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.setId (   self,
  args 
)
inherited

Python method signature(s):

setId(Model self, string sid)   int

Sets the value of the 'id' attribute of this Model.

The string sid is copied.

SBML has strict requirements for the syntax of identifiers, that is, the values of the 'id' attribute present on most types of SBML objects. The following is a summary of the definition of the SBML identifier type SId, which defines the permitted syntax of identifiers. We express the syntax using an extended form of BNF notation:
letter ::= 'a'..'z','A'..'Z'
digit  ::= '0'..'9'
idChar ::= letter | digit | '_'
SId    ::= ( letter | '_' ) idChar*
The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match; i.e., comparisons must be performed in a case-sensitive manner. In addition, there are a few conditions for the uniqueness of identifiers in an SBML model. Please consult the SBML specifications for the exact details of the uniqueness requirements.
Parameters
sidthe string to use as the identifier of this Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.Model.setLengthUnits (   self,
  args 
)
inherited

Python method signature(s):

setLengthUnits(Model self, string units)   int

Sets the value of the 'lengthUnits' attribute of this Model.

The string in units is copied.

Parameters
unitsthe new lengthUnits for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'lengthUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.SBase.setMetaId (   self,
  args 
)
inherited

Python method signature(s):

setMetaId(SBase self, string metaid)   int

Sets the value of the meta-identifier attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

The string metaid is copied.

Parameters
metaidthe identifier string to use as the value of the 'metaid' attribute
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getMetaId()
isSetMetaId()
def libsbml.SBase.setModelHistory (   self,
  args 
)
inherited

Python method signature(s):

setModelHistory(SBase self, ModelHistory history)   int

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters
historyModelHistory of this object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.Model.setName (   self,
  args 
)
inherited

Python method signature(s):

setName(Model self, string name)   int

Sets the value of the 'name' attribute of this Model.

The string in name is copied.

Parameters
namethe new name for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.setNamespaces (   self,
  args 
)
inherited

Python method signature(s):

setNamespaces(SBase self, XMLNamespaces xmlns)   int

Sets the namespaces relevant of this SBML object.

The content of xmlns is copied, and this object's existing namespace content is deleted.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Parameters
xmlnsthe namespaces to set
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.setNotes (   self,
  args 
)
inherited

Python method signature(s):

setNotes(SBase self, XMLNode notes)   int
setNotes(SBase self, string notes, bool addXHTMLMarkup=False)   int
setNotes(SBase self, string notes)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
setNotes(string notes, bool addXHTMLMarkup = false)

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:
setNotes(XMLNode notes)

Sets the value of the 'notes' subelement of this SBML object.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML structure that is to be used as the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.setSBOTerm (   self,
  args 
)
inherited

Python method signature(s):

setSBOTerm(SBase self, int value)   int
setSBOTerm(SBase self, string sboid)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
setSBOTerm(int value)

Sets the value of the 'sboTerm' attribute.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters
valuethe NNNNNNN integer portion of the SBO identifier
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setSBOTerm()

Method variant with the following signature:
setSBOTerm(string &sboid)

Sets the value of the 'sboTerm' attribute by string.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters
sboidthe SBO identifier string of the form 'SBO:NNNNNNN'
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setSBOTerm()
def libsbml.Model.setSubstanceUnits (   self,
  args 
)
inherited

Python method signature(s):

setSubstanceUnits(Model self, string units)   int

Sets the value of the 'substanceUnits' attribute of this Model.

The string in units is copied.

Parameters
unitsthe new substanceUnits for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.setTimeUnits (   self,
  args 
)
inherited

Python method signature(s):

setTimeUnits(Model self, string units)   int

Sets the value of the 'timeUnits' attribute of this Model.

The string in units is copied.

Parameters
unitsthe new timeUnits for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'timeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.setVolumeUnits (   self,
  args 
)
inherited

Python method signature(s):

setVolumeUnits(Model self, string units)   int

Sets the value of the 'volumeUnits' attribute of this Model.

The string in units is copied.

Parameters
unitsthe new volumeUnits for the Model
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'volumeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.SBase.toSBML (   self)
inherited

Python method signature(s):

toSBML(SBase self)   string *

Returns a string consisting of a partial SBML corresponding to just this object.

Returns
the partial SBML that describes this SBML object.
Warning
This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.
def libsbml.SBase.toXMLNode (   self)
inherited

Python method signature(s):

toXMLNode(SBase self)   XMLNode

Returns this element as an XMLNode.

Returns
this element as an XMLNode.
Warning
This operation is computationally expensive, because the element has to be fully serialized to a string and then parsed into the XMLNode structure. Attempting to convert a large tree structure (e.g., a large Model) may consume significant computer memory and time.
def libsbml.SBase.unsetAnnotation (   self)
inherited

Python method signature(s):

unsetAnnotation(SBase self)   int

Unsets the value of the 'annotation' subelement of this SBML object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
def libsbml.Model.unsetAreaUnits (   self)
inherited

Python method signature(s):

unsetAreaUnits(Model self)   int

Unsets the value of the 'areaUnits' attribute of this Model.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'areaUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.unsetConversionFactor (   self)
inherited

Python method signature(s):

unsetConversionFactor(Model self)   int

Unsets the value of the 'conversionFactor' attribute of this Model.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'conversionFactor' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.SBase.unsetCVTerms (   self)
inherited

Python method signature(s):

unsetCVTerms(SBase self)   int

Clears the list of CVTerm objects attached to this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.Model.unsetExtentUnits (   self)
inherited

Python method signature(s):

unsetExtentUnits(Model self)   int

Unsets the value of the 'extentUnits' attribute of this Model.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'extentUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.unsetId (   self)
inherited

Python method signature(s):

unsetId(Model self)   int

Unsets the value of the 'id' attribute of this Model.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.Model.unsetLengthUnits (   self)
inherited

Python method signature(s):

unsetLengthUnits(Model self)   int

Unsets the value of the 'lengthUnits' attribute of this Model.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'lengthUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.SBase.unsetMetaId (   self)
inherited

Python method signature(s):

unsetMetaId(SBase self)   int

Unsets the value of the 'metaid' attribute of this SBML object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.unsetModelHistory (   self)
inherited

Python method signature(s):

unsetModelHistory(SBase self)   int

Unsets the ModelHistory object attached to this object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.Model.unsetName (   self)
inherited

Python method signature(s):

unsetName(Model self)   int

Unsets the value of the 'name' attribute of this Model.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.unsetNotes (   self)
inherited

Python method signature(s):

unsetNotes(SBase self)   int

Unsets the value of the 'notes' subelement of this SBML object.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.unsetSBOTerm (   self)
inherited

Python method signature(s):

unsetSBOTerm(SBase self)   int

Unsets the value of the 'sboTerm' attribute of this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.Model.unsetSubstanceUnits (   self)
inherited

Python method signature(s):

unsetSubstanceUnits(Model self)   int

Unsets the value of the 'substanceUnits' attribute of this Model.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'substanceUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.unsetTimeUnits (   self)
inherited

Python method signature(s):

unsetTimeUnits(Model self)   int

Unsets the value of the 'timeUnits' attribute of this Model.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'timeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.
def libsbml.Model.unsetVolumeUnits (   self)
inherited

Python method signature(s):

unsetVolumeUnits(Model self)   int

Unsets the value of the 'volumeUnits' attribute of this Model.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
The 'volumeUnits' attribute is available in SBML Level 3 but is not present on Model in lower Levels of SBML.